Recent research has shown that polystyrene nanoplastics (PS-NPs) can inhibit plant growth and the development of crops, such as rice. In this study, we aimed to investigate the effects of PS-NPs of different particle sizes (80 nm, 200 nm, and 2 µm) and charges (negative, neutral, and positive) on rice growth, and to explore the underlying mechanisms and potential strategies for mitigating their impacts. Two-week-old rice plants were planted in a standard ½ Murashige-Skoog liquid medium holding 50 mg/L of different particle sizes and/or charged PS-NPs for 10 days, and the liquid medium without PS-NPs was used as control. The results showed that positively charged PS-NPs (80 nm PS-NH2) had the greatest impact on plant growth and greatly reduced the dry biomass, root length, and plant height of rice by 41.04%, 46.34%, and 37.45%, respectively. The positively charged NPs with a size of 80 nm significantly decreased the zinc (Zn) and indole-3-acetic acid (IAA, auxin) contents by 29.54% and 48.00% in roots, and 31.15% and 64.30% in leaves, respectively, and down-regulated the relative expression level of rice IAA response and biosynthesis genes. Moreover, Zn and/or IAA supplements significantly alleviated the adverse effects of 80 nm PS-NH2 on rice plant growth. Exogenous Zn and/or IAA increased seedlings’ growth, decreased PS-NPs distribution, maintained redox homeostasis, and improved tetrapyrrole biosynthesis in rice treated with 80 nm PS-NH2. Our findings suggest that Zn and IAA synergistically alleviate positively charged NP-induced damage in rice.